Some of the values you are trying to bin are outside the min and max
you have set. Admittedly the error message should be much clearer as
to what the problematic values are, but trying using the 'avg'
analysis command to look at the minimum and maximum values of what you
are trying to bin, e.g.
runanlysis avg amd_exp:1 amd_exp:2 out avg.dat
Hope this helps,
-Dan
On Wed, Mar 15, 2023 at 9:54 AM Sayan Poddar via AMBER
<amber.ambermd.org> wrote:
>
> Dear AMBER developers and Users,
>
> I am receiving this warning message during PCA run through cpptraj
>
>
>
>
>
>
>
>
>
>
>
>
> *-- [hist amd_exp:1 amd_exp:2 min -150 max 150 bins 72 free 300 out
> amd_exp_free.dat] Calculating step from min=-150 max=150 bins=72. Dim
> amd_exp:1: -150.000000->150.000000, step 4.166667, 72 bins. Calculating
> step from min=-150 max=150 bins=72. Dim amd_exp:2: -150.000000->150.000000,
> step 4.166667, 72 bins. Hist: 10000 data points in each dimension. Hist:
> Allocating histogram, total bins = 5184 Warning: Frame 1 Coordinates out of
> bounds (-1) Warning: Frame 2 Coordinates out of bounds (-1) Warning: Frame
> 3 Coordinates out of bounds (-1) Warning: Frame 4 Coordinates out of bounds
> (-1)*
> *........*
>
>
>
>
>
>
>
> * Warning: Frame 5667 Coordinates out of bounds (-1) Warning: Frame 5668
> Coordinates out of bounds (-1) Warning: Frame 5669 Coordinates out of
> bounds (-1) Histogram: Calculating free E at 300.000000 K. Bins
> max is 74 Artificial ceiling (bin pop = 0.5) is 2.979144
> kcal/mol.TIME: Analyses took 0.0181 seconds.*
>
> Although I am getting the result in the end. But what is the meaning of
> this warning?
>
> *with regards*
> *Sayan Poddar*
>
> *PhD Research Scholar*
> *Department of Biosciences and Biomedical Engineering*
> *Indian Institute of Technology Indore*
> *India*
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
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Received on Wed Mar 15 2023 - 07:30:02 PDT
